Learning QIIME 2

[Hassan]

When you use QIIME2 with default pipeline methodologies:

How does it deal with PCR Chimeras?

How does it deal with eukaryotic and contaminant sequences?

Does it use any normalization methodology?

Please explain how to blast the results that I get from QIIME?

[jwdebelius (Justine Debelius)]

Hi @Hassan,

First, welcome to the forum!

First, I think one of the great (and sometimes challenging) things about QIIME 2 is that there isn't a default pipeline. There are some steps everyone with amplicon data will probably take, but selecting the best way to do that is up to you. That said, have you gone through the tutorials? The moving pictures and PD mice tutorials both address many of these questions.

Best,
Justine

[Hassan]

Please answer these questions

What is a normalization methodology?
It is important to perform?

[jwdebelius (Justine Debelius)]

Hi @Hassan,

Please post publicly so we can all engage in the discussion. Have you looked at the tutorials because both of the ones I linked deal with normalization. If you search the forum, you’ll also find a lot fo discussion, especially in “General Discussion” and “User Support”. Its a conversation that goes out at least every three months so there’s plenty to read.

Best,
Justine